Multisignal labeling reagents and processes and uses therefor

ABSTRACT

Provided are compounds comprising two DNA supramolecular binding molecules covalently joined by a linker group. Also provided are multisignal labeling reagents comprising (i) an oligomer of nucleotides or nucleotide analogs; (ii) a DNA supramolecular binding molecule noncovalently bound to the oligomer; and (iii) a first reactive group or a first partner of a first binding pair covalently bound to the oligomer. Additionally provided are methods of producing multisignal labeling reagents.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of Ser. No. 14/844,468, filed Sep. 3,2015, which is a divisional of Ser. No. 13/065,101, filed Mar. 14, 2011,now U.S. Pat. No. 9,156,986, which is a continuation-in-part applicationof U.S. application Ser. No. 12/399,393, filed Mar. 6, 2009, now U.S.Pat. No. 8,394,949, which is a divisional of U.S. application Ser. No.10/407,818, filed Apr. 3, 2003, now U.S. Pat. No. 7,514,551, each ofwhich is hereby incorporated by reference in its entirety.

BACKGROUND OF THE INVENTION (1) Field of the Invention

The present application generally relates to compositions useful asmultisignal labeling reagents. More particularly, these reagents areuseful in a number of biochemical applications, including attachingsignals to analyte-specific moieties, such as proteins and morespecifically, antibodies. These reagents are also useful in labelingsamples contemplated to be assayed in protein array systems. Theaddition of multiple signals in such reagents is useful in increasingdetection sensitivity.

(2) Description of the Related Art

The use of non-radioactive labels in biochemistry and molecular biologyhas grown exponentially in recent years. Among the various compoundsused as non-radioactive labels, aromatic dyes that produce fluorescentor luminescent signal are especially useful. Notable examples of suchcompounds include fluorescein, rhodamine, coumarin and cyanine dyes suchas Cy3 and Cy5. Composite dyes have also been synthesized by fusing twodifferent dyes together (Lee et al., (1992) Nucl. Acids Res.20:2471-2488; Lee et al., U.S. Pat. No. 5,945,526 and Waggoner et al.,in U.S. Pat. No. 6,008,373, all of which are hereby incorporated byreference).

Non-radioactive labeling methods were initially developed to attachsignal-generating groups onto proteins. This was achieved by modifyinglabels with chemical groups such that they would be capable of reactingwith the amine, thiol, and hydroxyl groups that are naturally present onproteins. Examples of reactive groups that were used for this purposeincluded activated esters such as N-hydroxysuccinimide esters,isothiocyanates and other compounds. Consequently, when it becamedesirable to label nucleotides and nucleic acids by non-radioactivemeans, methods were developed to convert nucleotides and polynucleotidesinto a form that made them functionally similar to proteins. Forinstance, U.S. Pat. No. 4,711,955 (incorporated by reference) disclosedthe addition of amines to the 8-position of a purine, the 5-position ofa pyrimidine and the 7-position of a deazapurine. The same methods thatcould add a label to the amine group of a protein could now be appliedtowards these modified nucleotides.

Labeled nucleotides have been used for the synthesis of DNA and RNAprobes in many enzymatic methods including terminal transferaselabeling, nick translation, random priming, reverse transcription, RNAtranscription and primer extension. Labeled phosphoramidite versions ofthese nucleotides have also been used with automated synthesizers toprepare labeled oligonucleotides. The resulting labeled probes arewidely used in such standard procedures as northern blotting, Southernblotting, in situ hybridization, RNAse protection assays, DNA sequencingreactions, DNA and RNA microarray analysis and chromosome painting.

There is an extensive literature on chemical modification of nucleicacids by means of which a signal moiety is directly or indirectlyattached to a nucleic acid. Primary concerns of this art have been withregard to which site in a nucleic acid is used for attachment i.e.sugar, base or phosphate analogs and whether these sites are disruptiveor non-disruptive (see for instance the disclosures of U.S. Pat. No.4,711,955 and U.S. Pat. No. 5,241,060; both patents incorporated byreference), the chemistry at the site of attachment that allows linkageto a reactive group or signaling moiety a spacer group usuallyconsisting of a single aromatic group (U.S. Pat. Nos. 4,952,685 and5,013,831, both hereby incorporated by reference) or a carbon/carbonaliphatic chain to provide distance between the nucleic acid and areactive group or signaling moiety and a reactive group at the end ofthe spacer such as an OH, NH, SH or some other group that can allowcoupling to a signaling moiety and the nature of the signaling moiety.

More recently, U.S. Pat. No. 7,166,478 (incorporated by reference) hasdisclosed novel labeling reagents that comprise a reactive group capableof creating a carbon-carbon bond between a marker or label and adesirable target molecule. This is in contrast to labeling reagentsdescribed previously, which employed protein derived chemistriesinvolving formation of a bond between an amine, sulfhydryl or hydroxylgroup and an appropriate reactive group. The presence and nature of thelinker arm may also increase the biological or chemical activity of thelabeled target molecule. Linker arms that may be used to provideappropriate spacing of signal groups in nucleic acids were also providedin this disclosure.

BRIEF SUMMARY OF THE INVENTION

In some embodiments, a compound comprising two DNA supramolecularbinding molecules covalently joined by a linker group is provided. Thecompound further comprises a detectable label bound thereto, where thedetectable label is not either of the two DNA supramolecular bindingmolecules.

In other embodiments, a multisignal labeling reagent is provided. Themultisignal labeling reagent comprises (i) an oligomer of nucleotides ornucleotide analogs; (ii) a DNA supramolecular binding moleculenoncovalently bound to the oligomer; and (iii) a first reactive group ora first partner of a first binding pair covalently bound to theoligomer.

Also provided herein is a method of producing a multisignal labelingreagent. The method comprises (a) obtaining (i) a primer comprising anoligonucleotide and a first reactive group or a first partner of a firstbinding pair at the 5′ end of the oligonucleotide; (ii) a templatecomprising a nucleic acid comprising a first sequence that iscomplementary to the oligonucleotide and a second sequence that extendsin the 5′ direction from the first sequence; (iii) a polymerase capableof extending the oligonucleotide along the template nucleic acid whenthe template nucleic acid is hybridized to the oligonucleotide at thefirst sequence; and (iv) nucleotide triphosphates (NTPs) or analogsthereof that are capable of being incorporated into the extendedoligonucleotide, wherein at least one of the NTPs or analogs comprises anon-radioactive detectable label, a second reactive group or a firstpartner of a second binding pair; and (b) combining the primer,template, polymerase and NTPs or analogs under conditions such that theoligonucleotide hybridizes to the first sequence and is extended alongthe second sequence, where the extended oligonucleotide comprises atleast two NTPs or analogs incorporated therein that comprise anon-radioactive detectable label, a second reactive group or a firstpartner of a second binding pair. In these embodiments, (A) if at leastone of the two or more NTPs or analogs incorporated into the extendedoligonucleotide comprises a second reactive group, the method furthercomprises combining the extended oligonucleotide with a first compoundcomprising a non-radioactive detectable label covalently linked to amoiety capable of reacting with the second reactive group such that thelabel is covalently linked to the extended primer, and (B) if at leastone of the two or more NTPs or analogs incorporated into the extendedoligonucleotide comprises a first partner of the second binding pair,the method further comprises combining the extended primer with a secondcompound comprising the non-radioactive detectable label covalentlylinked to a second binding partner of the second binding pair.

Further provided is another method of producing a multisignal labelingreagent. This method comprises (a) obtaining (i) a primer comprising anoligonucleotide; (ii) a template comprising a nucleic acid comprising afirst sequence that is complementary to the oligonucleotide and a secondsequence that extends in the 5′ direction from the first sequence; (iii)a polymerase capable of extending the oligonucleotide along the templatenucleic acid when the template nucleic acid is hybridized to theoligonucleotide at the first sequence; (iv) nucleotide triphosphates(NTPs) or analogs thereof that are capable of being incorporated intothe extended oligonucleotide, wherein at least one of the NTPs oranalogs comprises a non-radioactive detectable label, a second reactivegroup or a first partner of a second binding pair; and (v) a polymercapable of binding to more than one of the extended oligonucleotide,wherein the polymer comprises a first reactive group or a first partnerof a first binding pair; (b) combining the primer, template, polymeraseand NTPs or analogs under conditions such that the oligonucleotidehybridizes to the first sequence and is extended along the secondsequence, where the extended oligonucleotide comprises at least two NTPsor analogs incorporated therein that comprise a non-radioactivedetectable label, a second reactive group or a first partner of a secondbinding pair; and (c) combining the extended oligonucleotide with thepolymer under conditions such that at least two of the extendedoligonucleotides bind to the polymer. In these embodiments, (A) if atleast one of the two or more NTPs or analogs incorporated into theextended oligonucleotide comprises a second reactive group, the methodfurther comprises combining the extended oligonucleotide with a firstcompound comprising a non-radioactive detectable label covalently linkedto a moiety capable of reacting with the second reactive group such thatthe label is covalently linked to the extended primer, and (B) if atleast one of the two or more NTPs or analogs incorporated into theextended oligonucleotide comprises a first partner of the second bindingpair, the method further comprises combining the extended primer with asecond compound comprising the non-radioactive detectable labelcovalently linked to a second binding partner of the second bindingpair.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows various arrangements of single-stranded and double-strandednucleic acid multisignal labeling reagents.

FIG. 2 is a diagram of an extended primer method of synthesizing amultisignal labeling reagent.

FIG. 3 is fluorescent micrographs of HeLa cells, SiHa cells and SK—N—SHcells stained with a multisignal labeling reagent prepared by theinvention extended primer method, where the multisignal labeling reagentwas designed to detect HPV 16/18 DNA integrated into the chromosome ofthe cells, where the cells have the indicated number of copies of theHPV 16/18 DNA.

DETAILED DESCRIPTION OF THE INVENTION

The present invention discloses methods and compositions for makinglabeled targets, labeled analytes and labeled analyte specific moietiesthat can have increased sensitivity and solubility compared to previousart. Examples of analyte specific moieties that may find use with thepresent invention can include but not be limited to nucleic acids,proteins, antibodies, antigens, ligands, receptors, hormones andsynthetic compounds. In one aspect of the present invention, novellabeling reagents are disclosed that comprise oligomers or polymers thatcomprise:

a) two or more labeled moieties where the label or labels are chemicallylinked to the oligomer or polymer

b) one or more reactive groups and

c) one or more charged groups that (i) are chemically linked to theoligomer or polymer or (ii) comprise part of the backbone of theoligomer or polymer or (iii) are any combination of the foregoing. Whenthe novel labeling composition or reagent is used to label a compoundfor detection of a specific analyte, the oligomer or polymer shouldsubstantially lack a specific affinity for the analyte.

The multiple labeled groups should increase the amount of signal that isadded to the analyte specific moiety; the presence of reactive groupswill allow attachment of the multiple labeled groups to a desirabletarget and the presence of a charged group should allow maintenance oran increase of solubility. Examples of useful chemical linkages forjoining labels or charged groups to the oligomer or polymer can includebut not be limited to covalent bonds, non-covalent bonds, ionic bonds,ligands, receptors and complexes. Examples of labels or markers caninclude but not be limited to fluorescent compounds or fluorophores,phosphorescent compounds, chemiluminescent compounds, chelatingcompounds, electron dense compounds, magnetic compounds, intercalatingcompounds and energy transfer compounds. With reference to solubility,many fluorescent compounds used as labels have extensive aromatic orhydrophobic character and the charge group or groups of the presentinvention can provide compensation for this property. Examples ofcharged groups that may be useful in providing solubility can includebut not be limited to phosphate, carboxylic, sulfone, amine and hydroxygroups. The charged groups can be an inherent part of the oligomer orpolymer or they can be non-inherent modifications that are artificiallyintroduced. Novel labeled analyte specific moieties may be used for thedetection of any analyte including but not limited to nucleic acids,proteins, antibodies, antigens, ligands, receptors, hormones and drugs.

Each of the monomeric units of the oligomer or polymer can comprise amarker or the oligomer or polymer may comprise a mixture of labeled andunlabeled monomeric units. A labeled monomeric unit can comprise asingle label or more than one label. When more than one label isincluded in a monomeric unit, they may be attached at the same site orat different sites on the monomer. An example of a monomeric unit withmore than one label at a single site is a nucleotide that has acomposite dye such as a fluorescein moiety linked to rhodamine moiety.On the other hand, the same methods used for making a composite dyedescribed in U.S. Patent Publication No. 2005/0137388, incorporatedherein by reference, could be applied to the synthesis of tandem dimers,trimers etc. of the same dye. As such, the user is able to direct thenumber of monomeric units, the proportion of labeled monomeric units,and the number of labels per monomer.

Examples of monomeric units that can be used to create an oligomeric orpolymeric labeling reagent can include but not be limited to aminoacids, nucleotides, carbohydrates, sugars, aromatic compounds and anyorganic compound that may be derivatized to be able to form oligomericor polymeric moieties. Modified versions or analogs of any monomericunits may also be used. Examples of analogs that might find use in thepresent invention can comprise but not be limited to nucleotide analogscomprising universal or degenerate bases (reviewed in Lockahart 2001,Nucl Acids Res 29:2437-2447), peptide nucleic acid monomers (Nielsen etal., 1991 Science 254:1497), non-nucleotide spacer groups (U.S. Pat. No.5,696,251), sugar analogs (Ono et al., 1997 Nucl Acids Res25:4581-4588), methylphosphonamidites (Loschner and Engels 1988Nucleosides Nucleotides 7:729) and phosphorothioates (Stec et al., 1984J Am. Chem. Soc. 106:6077) all of which are incorporated by reference.

Examples of oligomers or polymers made from such monomeric units caninclude but not be limited to nucleic acids, abasic nucleic acids,peptide nucleic acids, polypeptides, proteins, oligosaccharides,polysaccharides and organic polymers. The oligomers or polymers used inthe present invention may be isolated from biological sources or theymay be created synthetically or in vitro. It may be desirable that thelabels and/or reactive groups that are chemically linked to theoligomers or polymers are not intrinsic to such oligomers and polymers.The oligomers or polymers may be homopolymeric and comprise multiples ofonly one particular type of monomeric unit or they may beheteropolymeric or chimeric and comprise different monomeric units. Forexample, a chimeric oligomer or polymer can be a nucleic acid constructthat comprises both a normal nucleic acid segment and a peptide nucleicacid segment, a combination of nucleotides and amino acids or acombination of a segment of an abasic nucleic acid and a segmentcomprising a peptide nucleic acid. The present invention finds especialuse when the labeling reagent of the present invention is used to labelan oligomeric or polymeric target molecule, where the monomeric units ofthe labeling reagent may have a different nature from the monomericunits of the oligomeric or polymeric target. As an example of this, theoligomeric or polymeric moieties can be nucleic acid constructs thatcomprise labeled nucleotides or nucleotide analogs and at least onereactive group thereby providing the ability to attach multiple labelsto one or more of the amino acids that make up a target protein. Any ofthe markers, linkers and reactive groups that had been disclosedpreviously in the literature may find use in this particular embodimentof the present invention.

Additionally, even when the monomeric units of an oligomer or polymermay be of a similar nature, they may be the same or they may bedifferent. For instance a nucleic acid polymer may be a homopolymercomprising a reiteration of a single base or it can be a heteropolymerhaving varied nucleotides. A polypeptide may be homopolymeric andcomprise multiples of a single amino acid or it may be heteropolymericand comprise different amino acids. The labels in an oligomeric orpolymeric labeling reagent may also be the same or they may bedifferent. For instance, a labeling reagent that comprises two differentdyes attached at discrete intervals on a polynucleotide may participatein energy transfer for signal generation.

Oligomers or polymers of the present invention may comprise a singlechain structure linking the monomeric units together or they maycomprise more than one chain. For example, branched, double-stranded andtriple-stranded nucleic acids may all find use with present invention.Such multi-chain structures may provide useful properties. For example,a double-stranded nucleic acid is more rigid than a single strandednucleic acid. The use of a double-stranded structure may allow bettercontrol over the distribution or spacing of labeled moieties whereproximity or lack of proximity may be desirable. For instance, efficientsignal generation by means of energy transfer depends upon a closeproximity of donor and acceptor moieties and as such, establishment of aproximity between these moieties can be beneficial. On the other hand,if a single dye species is being used as signal generators, a closeproximity of some dye molecules can lead to a self-quenching phenomenonand spreading out the locations of the dyes could be beneficial. The useof more than one chain may also convey other useful properties such asincreasing the amount of signal generated or increasing the chargenumber. Multiple chains may also endow the system with flexibility ofuse. For example, a first nucleic acid strand may comprise a reactivegroup and a second nucleic acid strand with complementary sequences cancomprise signal groups. By complementary base pairing between thesestrands, a complex can be formed that comprises a reactive group andsignaling groups. To illustrate these points further, some variations onthe use of multiple chains are shown in FIG. 1. The use of multiplechains for the novel labeling reagent of the present invention can beextended further in preparation of reagents or labeled moieties that canbe used in parallel. For instance, a first chain comprising a reactivegroup can be mixed with either of two second chains to prepare twodifferent compounds that use the same reactive group but compriseddifferent labels from each other. The oligomers and polymers of thepresent invention may also comprise non-polymeric components as well.For example, they may comprise termini or extended chains with extendedmultiple charged groups. Other groups that may offer useful additionalproperties may also find use with the present invention.

Previous art has disclosed the use of nucleic acids as labeling agentsfor proteins (U.S. Patent Publication 2010/0273145). However, themethods in that reference described the attachment of an unlabeledpolynucleotide to targets followed by hybridization of labeledcomplementary nucleic acids. In contrast, in the present invention, whena complex comprising two or more oligonucleotides or polynucleotides isused to convey multiple signals, a preformed reagent is used thatcomprise the signals as well as one or more reactive groups. In thisway, the target doesn't proceed through a hybridization reaction. Themethodology also allows purification of the complex prior to attachmentto a target insuring that there is maximal amount of labeled nucleicstrands in the complexes with reactive groups. Due to an interest inlabeling nucleic acids, a wide variety of techniques are known in theart for joining nucleic acids to non-nucleic acids. Examples of suchmethods are disclosed in Jablonski et al., 1986 Nucl acids Res 14;6115-6128, U.S. Patent Publications 2004/0161741 and 2010/0273145, and“Methods for Nonradioactive Labeling of Nucleic Acids” by ChristopherKessler pp 42-109 in Nonisotopic Probing, Blotting and Sequencing,2^(nd) edition, Larry J. Kricka (Ed.), 1995, Academic Press, Inc., SanDiego, Calif., all of which are hereby incorporated by reference.

It is a further aspect of the present invention that when the oligomeror polymer is a nucleic acid, the reactive group may be replaced by abinding partner. Thus, the interaction of a binding partner in thelabeling reagent with its binding partner counterpart on the targetmolecule will allow attachment of the labels to the target molecule.Examples of binding partner pairs can include but not be limited toligand/receptor, hormone/receptor, biotin/avidin, biotin/streptavidinand antigen/antibody pairs.

As such, in this aspect of the present invention, a novel labelingreagent is disclosed that comprises a nucleic acid strand or a complexof nucleic acid strands which further comprises two or more labels andone or more binding partners where the binding partners may be differentfrom the labels or they may be the same. This aspect of the presentinvention finds especial use where the labeled nucleic acid strand orcomplex is linked to a non-nucleic acid target by means of a bindingpartner. Thus although previous art has described the ability to labelnucleic acids by binding labeled proteins, this aspect of the presentinvention discloses the ability to label proteins by binding labelednucleic acids.

In a further aspect of the present invention, the novel or oligomeric orpolymeric units comprise one or more reactive groups R which may beconnected by linker arm L which is a chain of atoms of any length thatmay be comprised of carbon, nitrogen, oxygen, sulfur in any combinationand any other possible atom. The connecting chain can be saturated,unsaturated or can contain aromatic rings and the linking chain can beflexible or rigid. The connecting chain can further comprise any of therigid units previously disclosed in U.S. Patent Publication2005/0137388. In this aspect of the invention, examples of reactivegroups can include but not be limited to active esters, groups capableof forming a carbon-carbon bonds and groups capable of forming bondswith O, N or S. Examples of such groups can include but not be limitedto isothiocyanate, isocyanate, monochlorotriazine, dichlorotriazine,mono- or di-halogen substituted pyridine, mono- or di-halogensubstituted diazine, maleimide, aziridine, sulfonyl halogen substituteddiazine, maleimide, aziridine, sulfonyl halide, acid halide,hydroxysuccinimide ester, hydroxysulfosuccinimide ester, imido ester,hydrazine, azidonitrophenyl, azide, 3-(2-pyridyl dithio)-proprionamide,glyoxal, aldehyde, carbon-carbon double bonds, mercury salts, and anygroup capable of reacting with carbon-carbon double bonds, amines,hydroxyl groups, sulfhydryl groups and halogens. The reactive groups mayalso participate in formation of a coordinate bond when R comprises aligand or a metal. A reactive group R can be attached to the oligomericor polymeric moiety through a linker arm L as described above or ifdesired it may be attached directly without the use of a linker arm. Itis a further aspect of this invention that the reactive group can bechemically linked to the novel labeling reagent at a terminus, a sidechain or an internal site of the oligomeric or polymeric moiety.Furthermore, the novel polymeric composition described may also containadditional alkyl, aryl and/or polar or charged groups on the backbone,linking arm or the dyes or labels. The polar or charged groups mayinclude but are not limited to halogen, substituted or unsubstitutedalkyl or aryl groups, saturated or unsaturated alkyl groups, alkoxy,phenoxy, amino, amido, and carboxyl groups, polar groups such asnitrates, sulfonates, sulfhydryl groups, nitrites, carboxylic acids,phosphates or any other such group or substitutent.

In another aspect of the present invention, the novel oligomeric orpolymeric labeling reagents can be described as follows:

In the diagram above, Q refers to a charged group and n is equal to aninteger of 1 or greater; D refers to a dye or other suitable label and mis equal to or greater than 2; R refers to at least one reactive groupthat may be used to join the labeling reagent to a suitable target and Prepresents the oligomer or polymer. The charged groups and dyes may beattached to each of the monomeric units that comprise P or only some ofthe monomeric units may comprise these groups.

In another aspect of the present invention, the novel oligomeric orpolymeric labeling reagents can be described as follows:

In the diagram above, D refers to a dye or other suitable label and m isequal to or greater than 2; R refers to at least one reactive group; Prepresents the oligomer or polymer and where D or one of the monomericunits of P comprises one or more charged groups. The dyes may beattached to each of the monomeric units that comprise P or only some ofthe monomeric units may comprise these groups.

In another aspect of the present invention, novel compositions of theform shown below are disclosed where the novel oligomeric or polymericlabeling reagents of the present invention have been used to labelsuitable target molecules.

In the diagram above, Q refers to a charged group and n is equal to aninteger of 1 or greater; D refers to a dye or other suitable label and mis equal to or greater than 2; P represents an oligomer or polymer; andL is the linkage that joins the labeling reagent to the target molecule.The charged groups and dyes may be attached to each of the monomericunits that comprise P or only some of the monomeric units may comprisethese groups. L may comprise any of the linkage arms describedpreviously or it may comprise the linkage formed between a reactivegroup R and the appropriate chemical group on the target molecule. Thetarget can be chosen from a group that includes but is not limited topeptides, proteins, antibodies, enzymes, enzyme substrates, ligands,hormones, receptors, antigens, haptens, lectins, avidin, streptavidin,lipids, lipoproteins, glycoproteins, proteoglycans, nonpolymeric organiccompounds, toxins, carbohydrates, oligosaccharides, polysaccharides,ribonucleotides, deoxyribonucleotides, dideoxyribonucleotides, analogsof deoxynucleotides, ribonucleotides and dideoxynucleotides, modifieddeoxynucleotides, modified ribonucleotides, modified dideoxynucleotidesoligonucleotides, polynucleotides, and any other analyte specific moietythat can form a linkage with the reactive group R.

In another aspect of the present invention, novel compositions of theform shown below are disclosed where the novel oligomeric or polymericlabeling reagents of the present invention have been used to labelsuitable target molecules:

In the diagram above, D refers to a dye or other suitable label and m isequal to or greater than 2; P represents an oligomer or polymer; L isthe linkage that joins the labeling reagent to the target molecule andwhere D or one of the monomeric units of P comprises one or more chargedgroups. The dyes may be attached to each of the monomeric units thatcomprise P or only some of the monomeric units may comprise thesegroups. L may comprise any of the linkage arms described previously orit may comprise the linkage formed between a reactive group R and theappropriate chemical group on the target molecule. The target may bechosen from any members of the group described previously.

The various aspects of the present invention that provide multiplesignals allow the synthesis of highly sensitive labeling compositions.In methods previously used for preparing labeled reagents such asenzymatic incorporation, the number of dye units is often limitedbecause of poor incorporation of the dye by the enzyme. Furthermore, itis also possible for two or more dye units to be placed adjacent to eachother after enzymatic incorporation, which often results in thequenching of the signal. One advantage of the present invention is thatthe placement of the dyes can be specifically controlled so that therequired number of dye units and spacing between them can be designedfor optimal signal. This can result in labeling reagents with labeledunits that produce the maximum amount of signal with minimal quenchingfrom adjacent units. The novel labeling reagents of the presentinvention can be used for a wide variety of purposes where increasedsignal strength is beneficial.

It is a further aim of the present invention to provide unlabeledreagents that can be used in conjunction with the present invention orwith other labeling reagents or labeled materials. For instance, when acompound comprises a target specific moiety and a label, the highestlevel of signal to noise (S/N) is achieved when binding takes placethrough the agency of the target specific moiety and not through thelabel itself, or any components used to join the label to the targetspecific moiety. By definition, any part of the compound that is nottarget specific is incapable of discrimination and binding of suchmoieties to non-target molecules could potentially lead to a rise inbackground signal generation and a subsequent lowering of the S/N ratio.Therefore, the present invention discloses that unlabeled oligomeric andpolymeric compounds that are similar to labeled oligomeric or polymericmoieties used to label target specific moieties can be used in assaysdetecting the presence or quantity of a particular analyte where theunlabeled oligomers or polymers can suppress non-specific binding by theoligomers or polymeric components of labeled compounds.

As an illustrative example of this method, an antibody labeled with anoligonucleotide comprising multiple fluorescent moieties, e.g.,fluorescein, Texas Red, TAMRA (tetramethyl rhodamine), or rhodamine 110,is used as a detection reagent. Nonspecific binding can be blocked byany means known in the art, for example with unlabeled oligonucleotides,or with control oligonucleotides incorporating nonfluorescent analogs ofthe fluorescent moieties, e.g., 0,0-dimethyl fluorescein, N,N-diacetylrhodamine 110. The blocking reagent can be used either prior to orduring exposure of the specimen to the antibody detection reagent. Thenucleic acid can be a heterogeneous collection of sequences. Forinstance, salmon sperm or calf thymus DNA has commonly been used inassays with labeled DNA probes to eliminate non-specific general bindingof nucleic acids. Conversely, the sequence of the nucleic acid used tolabel the antibody could also be used for a blocking reagent, i.e. adiscrete sequence. It is also understood that combinations or mixturesof discrete, random, permutational or heterogeneous nucleic acids may beused for this purpose.

Also provided herewith are compounds useful for labeling nucleic acids.The compounds utilize DNA supramolecular binding molecules, which arecompounds that non-covalently bind to DNA, where the binding is not byWatson-Crick complementary pairing. Nonlimiting examples of DNAsupramolecular binding molecules are minor groove binders, major groovebinders, and intercalators. See, e.g., Hannon, 2007, Chem. Soc. Rev.36:280-295. These molecules bind to DNA, in some cases at specificsequences, often with a high binding affinity. The present inventionprovides two DNA supramolecular binding molecules covalently joined toeach other and further comprising a detectable label. By joining two DNAsupramolecular binding molecules together such that both molecules canbind DNA, the binding affinity of the dimer for DNA increases over thebinding affinity of each individual molecule, such that the compounddisplays very tight DNA binding. See, e.g., Capelle et al., 1979,Biochemistry 18:3354-3362. Although many DNA supramolecular bindingmolecules are fluorescent such that they can serve as a labelthemselves, the detectable label included with the two DNAsupramolecular binding molecules in the present invention allows for theprovision of any desired label. The resulting molecule, when combinedwith the appropriate nucleic acid, spontaneously binds very tightly tothe nucleic acid with the desired label. These compounds thus provide areagent that easily labels nucleic acids with any desired label.

Thus, in various embodiments, the present invention is directed to acompound comprising two DNA supramolecular binding molecules covalentlyjoined by a linker group. In these embodiments, the compound furthercomprises a detectable label bound thereto, where the detectable labelis not either of the two DNA supramolecular binding molecules.

In some embodiments, at least one of the DNA supramolecular bindingmolecules is a minor groove binder. Any minor groove binders known inthe art can be used in these compounds. In some embodiments, the minorgroove binder is a diacrylamidine, or a bis-benzimidazole. In morespecific embodiments, the minor groove binder is DAPI, berenil,pentamidine, distamycin A, or Hoechst 33258.

In other embodiments, at least one of the DNA supramolecular bindingmolecules is a major groove binder. Any major groove binder can beutilized in these embodiments. Nonlimiting examples include a moleculecomprising a zinc finger, a leucine zipper or a helix-turn-helix motif.

In additional embodiments, at least one of the DNA supramolecularbinding molecules is an intercalator. Publications describing the use ofintercalating dyes in studies using nucleic acids include Georghiou,Photochem. Photobiol. 26:59-68 (1977); Kubota et al., Biophys. Chem.,6:279-284 (1977); Genest et al., Nucl. Acid Res., 13:2603-2615 (1985);Asseline, EMBO J. 3:795-800 (1984); and U.S. Pat. Nos. 4,257,774 and4,547,569.

In some of these embodiments, both of the DNA supramolecular bindingmolecules are intercalators, either the same or different intercalators.

These embodiments are not narrowly limited to any particular DNAintercalators. Nonlimiting examples of classes of intercalators that maybe used in these embodiments are acridines, coumarins, psoralens,quinoxalines, phenanthridines, anthracyclines, or metallo-intercalators,as they are known in the art (see, e.g., Hannon et al., Id.). Particularuseful intercalators include 9-aminoacridine,7-hydroxy-4-methylcoumarin, 7-amino-4-methylcoumarin,4-methyl-7-sulphato-methylcoumarin,8-[[[(diethylamino)methyl]propyl]oxy]psoralen,5(N-piperadinyl)-8-methoxypsoralen, ethidium bromide, thiazole orange,6-(-4′-carboxyphenyl)-3,8-diamine-5-methyl phenanthridinium chloride,doxorubicin, daunomycin, [Pt(tpy)(SCH₂CH₂OH)]⁺, and[Rh(phi)(Me₂trien)]³⁺.

The linker in these compounds not only links the two DNA supramolecularbinding molecules but can also serve to separate the two molecules sothat both of the molecules can bind to a nucleic acid. For example, itis well known that DNA intercalators can be inserted into DNA at amaximum of one intercalator per two basepairs. Consequently, where twointercalators are used with these compounds, the linker preferablyseparates those intercalators at a distance of at least two basepairs,so that they can both insert into the nucleic acid. Such linkers areknown in the art and have been utilized with several dimericintercalators. See, e.g., Canellakis and Bellantone, 1976, Biochim.Biophys. Acta 418:290-299; Canellakis et al., 1976, BiochemicalPharmacol. 25:231-236; Canellakis et al., 1976, Biochim. Biophys. Acta418:277-289; Canellakis et al., 1976, Biochim. Biophys. Acta418:300-314; Fico et al., 1977, Science 198:53-56; Wakelin et al., 1978,Biochemistry 17:5057-5063; Gaugain et al., 1978, Biochemistry17:5071-5087; Gaugain et al., 1978, Biochemistry 17:5078-5088; Chen etal., 1978, J. Medicinal Chem. 21:868-874; Capelle et al., 1979,Biochemistry 18:3354-3362; Wright et al., 1980, Biochemistry19:5825-2836; King et al., 1982, Biochemistry 21:4982-4989; Timtcheva etal., 2000, J. Photochem. Photobiol. B:Biology 58:130-135; Moloney etal., 2001, Molecules 6:230-243.

Similar considerations apply to other DNA supramolecular bindingmolecules—the linker is preferably of sufficient length so that bothmolecules can bind to a nucleic acid.

The linker in these compounds can be rigid or flexible. Rigid linkershave been utilized with dimer intercalators. See, e.g., Glover et al.,2003, J. Am. Chem. Soc. 125:9918-9919. However, flexible linkers do notrequire the precise design required of rigid linkers, where the linkermust precisely separate and orient the DNA supramolecular bindingmolecules to properly insert into the nucleic acid.

In some embodiments, the linker is an unsubstituted C₁-C₂₀straight-chain, branched or cyclic alkyl, alkenyl or alkynyl group, asubstituted C₁-C₂₀ straight-chain, branched or cyclic alkyl, alkenyl oralkynyl group wherein one or more C, CH or CH₂ groups are substitutedwith an O atom, N atom, S atom, NH group, CO group or OCO group, or anunsubstituted or substituted aromatic group. In more specificembodiments, the linker is —(CH₂)₁₋₁₀—NH—(CH₂)₁₋₁₀—. In still morespecific embodiments, the linker is —(CH₂)₁₋₅—NH—(CH₂)₁₋₅—. One usefullinker within these embodiments is —(CH₂)₃—NH—(CH₂)₄— (spermidine—seeExamples 20-22 and the exemplary compounds described below).

Any detectable label now known or later discovered may be utilized forthese compounds. In some embodiments, the detectable label isradioactive. The radioactive label can be part of the compound (e.g.,³H, or ¹⁴C), or can be attached thereto (e.g., ¹³¹I).

In other embodiments, the detectable label is non-radioactive.Non-limiting examples include fluorescent compounds, phosphorescentcompounds, chemiluminescent compounds, chelating compounds, electrondense compounds, magnetic compounds, and energy transfer compounds, asthey are known in the art.

In various embodiments, the non-radioactive detectable label is afluorophore. Any fluorophore now known or later discovered can beutilized in these compounds. Examples of useful fluorophores includewithout limitation a symmetric or asymmetric cyanine dye, a merocyaninedye, a styryl dye, an oxazine dye, a xanthene dye, a coumarin dye or animinocoumarin dye.

One class of fluorophore useful in the invention has a xanthene backboneshown in Scheme I below. The structures are shown in their lactone forms(A) as well as aphenylic counterparts, which have their appended phenylring missing (B).

The substituents R¹, R² and R³ in Scheme I represent a variety offunctionalities where R³ may be a reactive group, which allows theattachment to other moieties, e.g., the linker. The R¹s and R²s may bestructurally the same or different; there may be more than one R² oneither or both rings. An R² group can join with an R¹ group to form aring. Suitable examples of R¹ include but are not limited to hydrogen,OH, OR⁴, NH₂, NHR⁴, or NR⁴R⁴ where each R⁴ is independently astraight-chain, branched or cyclic C₁-05 alkyl group, optionally furthercomprising a carboxyl or carbonyl (COR⁵) group, where R⁵ is hydrogen, anoptionally substituted straight-chain, branched or cyclic alkyl, alkenylor alkynyl group, where one or more C, CH or CH₂ groups can be replacedwith an O atom, an N atom, an S atom, a NH group, a CO group, an OCOgroup, a CONR⁶ group, or an optionally substituted aromatic group, whereR⁶ is a straight-chain, branched or cyclic alkyl, alkenyl or alkynylgroup. Suitable examples of R² and R³ include but are not limited tohydrogen, a halogen (F, Cl, Br, I), a cyano group (CN), a nitro group(NO²), an isocyano group (NC), a thiocyano group (SCN), an isothiocyanogroup (SNC), a sulfonate group (SO₃R⁷), a sulfate group (OSO₃R⁷), acarboxyl group (CO₂H), an ester group (CO₂R⁷ or OCOR⁷), an amide group(CONR⁶ ₂ or NR⁶COR⁷), a carbamate group (NR⁷CO₂R⁷ or OCONR⁷ ₂), aphosphate group (OPO₃R⁷ ₃), a phosphonate group (PO₃R⁷ ₂), an alkoxygroup (OR⁷), a sulfoxy group (SOR⁷), a sulfone group (SO₂R⁷), asulfonamide group (SO₂NR⁷ ₂), an optionally substituted straight-chain,branched or cyclic alkyl, alkenyl or alkynyl group wherein one or moreC, CH or CH₂ groups can be replaced with O atom, N atom, CO group, OCOgroup, CONIC group, or an optionally substituted aromatic group. Inthese embodiments, each R⁷ is independently hydrogen, an optionallysubstituted straight-chain, branched or cyclic alkyl, alkenyl or alkynylgroup wherein one or more C, CH or CH₂ groups can be replaced with Oatom, N atom, CO group, OCO group, CONR⁶ group, or an optionallysubstituted aromatic group.

As discussed above, the R³ group is, or can be substituted to contain, areactive group thereby allowing the fluorophore to be chemically boundto the linker or one or both intercalators. Examples of reactive groupsthat may find use in the present invention can include but not belimited to a nucleophilic reactive group, an electrophilic reactivegroup, a terminal alkene, a terminal alkyne, a platinum coordinate groupor an alkylating agent.

There are a number of different electrophilic reactive groups that mayfind use in these embodiments. Examples include but not be limited toisocyanate, isothiocyanate, monochlorotriazine, dichlorotriazine,4,6,-dichloro-1,3,5-triazines, mono- or di-halogen substituted pyridine,mono- or di-halogen substituted diazine, maleimide, haloacetamide,aziridine, sulfonyl halide, acid halide, hydroxysuccinimide ester,hydroxysulfosuccinimide ester, imido ester, hydrazine, azidonitrophenol,azide, 3-(2-pyridyl dithio)-proprionamide, glyoxal and aldehyde groups.Nucleophilic reactive groups can include but not be limited to reactivethiol, amine and hydroxyl groups. For purposes of synthesis of dyes,reactive thiol, amine or hydroxyl groups can be protected during varioussynthetic steps and the reactive groups generated after removal of theprotective group.

One class of xanthene fluorophores useful in the present inventionincludes but not limited to rhodamine and rhodamine derivatives, such asPennsylvania Green, Tokyo Green, Oregon Green, Singapore Green, androsamines and rhodols and their derivatives. Some of these derivativesare shown below in Scheme II. The rhodamine, rosamine and rhodolbackbone structures can be extended by adding additional rings as shownin Scheme III, or their appended phenyl ring might be missing to formaphenylic counterparts.

Another class of fluorescent dyes pertinent to the present invention isbased on coumarin and iminocoumarin backbone structure shown in SchemeIV.

The substituent R² in Scheme IV represents functionalities defined inScheme I above while A can be an O atom, or imino group, NH. Some of thecompounds in this category are shown below in Scheme V. The backbonestructure can be extended by adding additional rings, aliphatic oraromatic, substituted or unsubstituted.

In other embodiments of the compounds of the present invention, thedetectable label is a luminescent moiety. Any luminescent moiety,including any chemiluminescent or bioluminescent moieties, now known orlater discovered, can be utilized in these embodiments. In some aspectsof these embodiments, the compound comprises the structure:

The substituents R² and R⁵ in these structures represent functionalitiesdefined in Scheme I above.

In some embodiments, the detectable label is bound to the compound via abinding pair. A multitude of binding pairs is known in the art.Nonlimiting examples include ligand/receptors, hormone/receptors,biotin/avidin, biotin/streptavidin, and antigen/antibodies.

In other embodiments, the detectable label is covalently bound to thecompound, either to the linker group or to one or both of the DNAsupramolecular binding molecules. When bound to a DNA supramolecularbinding molecule, it is preferred that the detectable label does notinterfere, e.g., through steric hindrance, with the ability of the DNAsupramolecular binding molecule to bind to nucleic acids.

In various embodiments, these compounds comprise more than two DNAsupramolecular binding molecules and/or more than one detectable label.

Exemplary compounds comprising two intercalators and fluorescent labelsare

The ease with which the multisignal labeling reagents described hereincan be synthesized is directly related to the ease of binding thedetectable labels to the reagents. In this regard, DNA supramolecularbinding molecules bind spontaneously without any modification of thenucleic acid that makes up the backbone of various multisignal labelingreagents. This spontaneous binding of DNA supramolecular bindingmolecules forms the basis of particular embodiments of the instantinvention.

Thus, provided is a multisignal labeling reagent that comprises (i) anoligomer of nucleotides or nucleotide analogs; (ii) a DNA supramolecularbinding molecule noncovalently bound to the oligomer; and (iii) acovalently bound first reactive group or a first partner of a firstbinding pair.

In some of these embodiments, the DNA supramolecular binding molecule isfluorescent. Examples include most intercalators and the minor groovebinder DAPI. In these embodiments, the DNA supramolecular bindingmolecule itself can serve as a label, by virtue of its fluorescence. Inother embodiments, the DNA supramolecular binding molecule furthercomprises a detectable label that is not the supramolecular bindingmolecule. These latter embodiments allow the user to select the labelhaving the desired detection characteristics, such as fluorescenceemission maxima.

Any detectable label now known or later discovered may be utilized forthese reagents. In some embodiments, the detectable label isradioactive. The radioactive label can be part of the compound (e.g.,³H, or ¹⁴C), or can be attached thereto (e.g., ¹³¹I).

In other embodiments, the detectable label is non-radioactive.Non-limiting examples include fluorescent compounds, phosphorescentcompounds, chemiluminescent compounds, chelating compounds, electrondense compounds, magnetic compounds, and energy transfer compounds, asthey are known in the art.

In various embodiments, the non-radioactive detectable label is afluorophore. Any fluorophore now known or later discovered can beutilized in these reagents. Examples of useful fluorophores includewithout limitation a symmetric or asymmetric cyanine dye, a merocyaninedye, a styryl dye, an oxazine dye, a xanthene dye, a coumarin dye or animinocoumarin dye, as described above.

These multisignal labeling reagents can incorporate any DNAsupramolecular binding molecule known in the art. In some embodiments,the DNA supramolecular binding molecule is a minor groove binder. Anyminor groove binders known in the art can be used in these reagents. Insome embodiments, the minor groove binder is a diacrylamidine, or abis-benzimidazole. In other embodiments, the minor groove binder isDAPI, berenil, pentamidine, distamycin A, or Hoechst 33258.

In other embodiments, the DNA supramolecular binding molecule is a majorgroove binder. Any major groove binder can be utilized in theseembodiments. Nonlimiting examples include a molecule comprising a zincfinger, a leucine zipper or a helix-turn-helix motif.

In additional embodiments, the DNA supramolecular binding molecule is anintercalator, as described above. In some of these embodiments, theintercalator is an acridine, a coumarin, a psoralen, a phenanthridine,an anthracycline, or a metallo-intercalator. Particular usefulintercalators include 9-aminoacridine, 7-hydroxy-4-methylcoumarin,7-amino-4-methylcoumarin, 4-methyl-7-sulphato-methylcoumarin,8-[[[(diethylamino)methyl]propyl]oxy]psoralen,5(N-piperadinyl)-8-methoxypsoralen, ethidium bromide, thiazole orange,6-(-4′-carboxyphenyl)-3,8-diamine-5-methyl phenanthridinium chloride,doxorubicin, daunomycin, [Pt(tpy)(SCH₂CH₂OH)]⁺, and[Rh(phi)(Me₂trien)]³⁺.

It is envisioned that, in most cases, the multisignal labeling reagentsprovided here comprise multiple DNA supramolecular binding molecules.The multiple DNA supramolecular binding molecules on any particularmultisignal labeling reagent may be any combination of any DNAsupramolecular binding molecule or may be all the same DNAsupramolecular binding molecule. In some embodiments, the multisignallabeling reagent comprises the compound described above comprising twoDNA supramolecular binding molecules covalently joined by a linkergroup.

The oligomer of any multisignal labeling reagent described herein can beany form of nucleic acid or analog, provided the DNA supramolecularbinding molecule can bind thereto. Additionally, the oligomer can be anylength, for example less than 10 nucleotides, less than 20 nucleotides,less than 50 nucleotides, less than 100 nucleotides, or 100 or morenucleotides.

Many DNA supramolecular binding molecules bind DNA in a sequencepreferential or sequence specific manner. For example, manyintercalators have a preference for the AT sequence. See, e.g.,Hampshire and Fox, 2008, Anal. Biochem. 374:298-303. Also, major groovebinders generally have specific sequence requirements. See, e.g.,Christy and Nathans, 1090, Proc. Natl. Acad. Sci. USA 86:8737-8741. Sucha sequence preference or requirement should be considered when a nucleicacid that is used for binding of the invention compounds is designed.

The first reactive group or the first partner of the first binding pairof the multisignal labeling reagent described herein may be used to bindthe reagent to a target to label the target for detection, as describedabove. In some embodiments, the multisignal labeling reagent comprises afirst partner of a first binding pair. Nonlimiting examples include aligand/receptor, a hormone/receptor, biotin/avidin, biotin/streptavidinor an antigen/antibody. A preferred first partner of the first bindingpair is streptavidin. In other embodiments, the multisignal labelingreagent comprises a first reactive group, as described above.

In some embodiments, particularly where a multisignal labeling reagentcomprises only one oligomer, the first reactive group or the firstbinding partner of the first binding pair is covalently bound to theoligomer. In other embodiments, the multisignal labeling reagent furthercomprises a polymer to which two or more of the oligomers are bound,where the first reactive group or the first partner of the first bindingpair is covalently attached to the polymer. The polymer can be, e.g., aoligopeptide, a protein, a nucleic acid or analog such as anoligonucleotide or a polynucleotide, a lipid, a oligosaccharide, apolysaccharide, or a synthetic compound such as an organic polymer(e.g., a plastic). In some embodiments, the polymer is a nucleic acidand the two or more oligomers are bound to the polymer by complementaryhybridization, for example as illustrated in FIG. 1, diagram (b) or (d).

Also provided herein are methods for producing the multisignalinglabeling reagents described above. These methods provide for the use ofa primer, template, polymerase and labeled nucleotide triphosphates(NTPs) or analogs to prepare the oligonucleotide of the reagents, byhybridizing the primer to the template and extending the primer alongthe template using NTPs, at least one of which is labeled. One aspect ofthese methods, where the labeled oligonucleotide comprises astreptavidin for binding directly to a target molecule, is illustratedin FIG. 2; examples of these methods are provided in Examples 18 and 19.These methods fall in two general categories: (1) where a singleoligonucleotide comprising more than one label is designed to bind tothe target molecule; and (2) where multiple oligonucleotides, eachcomprising more than one label, is bound to a polymer, where the polymeris designed to bind to the target molecule. In these methods, the singleoligonucleotide (category 1) or polymer comprising multiple labeledoligonucleotides (category 2) is designed to bind to the target moleculethrough either a reactive group (termed “first reactive group” in thesemethods) or through a binding pair, where one partner of the bindingpair (“first partner of a first binding pair”) (e.g., streptavidin) isbound to the multisignal labeling reagent, and the other partner of thebinding pair (e.g., biotin) is bound to the target molecule. Thisprovides a branched multisignal labeling reagent, for example asillustrated in FIG. 1 and exemplified in Example 19.

It is also to be recognized that in these methods, the detectable label(e.g., a fluorescent dye) can be covalently bound to the NTPs or analogsduring the primer extension procedure. Alternatively, the NTPs oranalogs can comprise a reactive group (“second reactive group” herein)or a partner of a binding pair (“first partner of a second reactivegroup”) (e.g., biotin), to which the detectable label is attached aftersynthesis of the oligonucleotide (as described in steps (A) and (B) inthe methods provided below).

Thus, in some embodiments, a method of producing a multisignal labelingreagent is provided. The method comprises

-   -   (a) obtaining        -   (i) a primer comprising an oligonucleotide and a first            reactive group or a first partner of a first binding pair at            the 5′ end of the oligonucleotide;        -   (ii) a template comprising a nucleic acid comprising a first            sequence that is complementary to the oligonucleotide and a            second sequence that extends in the 5′ direction from the            first sequence;        -   (iii) a polymerase capable of extending the oligonucleotide            along the template nucleic acid when the template nucleic            acid is hybridized to the oligonucleotide at the first            sequence; and        -   (iv) nucleotide triphosphates (NTPs) or analogs thereof that            are capable of being incorporated into the extended            oligonucleotide, wherein at least one of the NTPs or analogs            comprises a non-radioactive detectable label, a second            reactive group or a first partner of a second binding pair;            and    -   (b) combining the primer, template, polymerase and NTPs or        analogs under conditions such that the oligonucleotide        hybridizes to the first sequence and is extended along the        second sequence, where the extended oligonucleotide comprises at        least two NTPs or analogs incorporated therein that comprise a        non-radioactive detectable label, a second reactive group or a        first partner of a second binding pair;    -   wherein,        -   (A) if at least one of the two or more NTPs or analogs            incorporated into the extended oligonucleotide comprises a            second reactive group, the method further comprises            combining the extended oligonucleotide with a first compound            comprising a non-radioactive detectable label covalently            linked to a moiety capable of reacting with the second            reactive group such that the label is covalently linked to            the extended primer, and        -   (B) if at least one of the two or more NTPs or analogs            incorporated into the extended oligonucleotide comprises a            first partner of the second binding pair, the method further            comprises combining the extended primer with a second            compound comprising the non-radioactive detectable label            covalently linked to a second binding partner of the second            binding pair.

This method can utilize any non-radioactive label now known or laterdiscovered. Examples of useful non-radioactive detectable labels arefluorophores, phosphorescent moieties, chemiluminescent moieties,chelating moieties, electron dense moieties, magnetic moieties, orenergy transfer moieties, as they are known in the art.

In some embodiments, the non-radioactive detectable labels arefluorophores, e.g., symmetric or asymmetric cyanines, merocyanines,styryl moieties, oxazines, xanthenes, coumarins or iminocoumarins, asdetailed above. In other embodiments, the non-radioactive detectablelabels are chemiluminescent or phosphorescent moieties, as discussedabove.

The oligonucleotide of the multisignaling labeling reagent produced bythis method can be comprised of any form of oligonucleotide or analogthat can be extended with a polymerase, including DNA, RNA, or analogsthereof. Additionally, the oligonucleotide can be of any length, forexample less than 10 nucleotides, less than 20 nucleotides, less than 50nucleotides, less than 100 nucleotides, or 100 or more nucleotides.Further, any polymerase can be used in these methods, provided thepolymerase is capable of extending the primer along the templateoligonucleotide.

In this method, the NTPs or analogs that are labeled with the label,second reactive group, or first binding partner of a second binding pairis preferably only one of the four NTPs or analogs used to extend theprimer. By using only one labeled NTP or analog of the four NTPs oranalogs used to extend the primer, the position of the labels can beprecisely controlled by designing the template oligonucleotide such thatthe planned labeled NTP or analog is at the desired position.

The at least two NTPs or analogs that are labeled on the extendedoligonucleotide of the multisignal labeling reagent can be incorporatedinto the oligonucleotide as NTPs or analogs comprising the detectablelabels or with the second reactive group or the first binding partner ofthe second binding pair.

Where NTPs or analogs comprising the second reactive group are utilized,the detectable label must subsequently be added by adding a compoundcomprising the non-radioactive detectable label covalently linked to amoiety capable of reacting with the second reactive group such that thelabel is covalently linked to the extended primer, as indicated in step(A) of the method. Nonlimiting examples of reactive groups useful hereinclude isothiocyanate, isocyanate, monochlorotriazine,dichlorotriazine, mono- or di-halogen substituted pyridine, mono- ordi-halogen substituted diazine, maleimide, aziridine, sulfonyl halogensubstituted diazine, maleimide, sulfonyl halide, acid halide,hydroxysuccinimide ester, hydroxysulfosuccinimide ester, imido ester,hydrazine, azidonitrophenyl, azide, 3-(2-pyridyl dithio)-proprionamide,glyoxal, aldehyde, mercury salt, or combinations thereof. Methods ofattaching detectable labels to NTPs or analogs in this manner are wellknown in the art and summarized above.

In some embodiments, each reactive group is connected to the NTPs oranalogs by a linker arm, also as described above.

Where NTPs or analogs comprising the first binding partner of the secondbinding pair are utilized, the detectable label must subsequently beadded by combining the extended primer with a compound comprising thenon-radioactive detectable label covalently linked to a second bindingpartner of the second binding pair, as indicated in step (B) of themethod. Binding pairs are further discussed above. A nonlimiting exampleof a first binding partner of the second binding pair is biotin.

In some embodiments, each first binding partner of the second bindingpair is connected to the NTPs by a linker arm.

As discussed above in relation to other multisignal labeling reagents,the multisignal labeling reagents described here can comprise anon-inherent charged group that increases the aqueous solubility of thereagent. Nonlimiting examples of such charged groups include phosphate,carboxylic acid, sulfone, amine and hydroxy groups.

As discussed above, the primer comprises a first reactive group or afirst partner of a first binding pair, to attach the multisignallabeling reagent to a target. Any reactive group as discussed above maybe utilized here. Where the primer comprises a first partner of a firstbinding pair, any binding pair, now known or later discovered, may beprovided with the primer. Examples include a ligand/receptor, ahormone/receptor, biotin/avidin, biotin/streptavidin and anantigen/antibody. A preferred first partner of a first binding pair isstreptavidin. See, e.g., Example 18.

For its ultimate use, these methods can further comprise combining themultisignal labeling reagent with a target molecule such that themultisignal labeling reagent is bound to the target by the firstreactive group or the first partner of the first binding pair. Thetarget may be any compound to which a detectable label is desired.Nonlimiting examples of targets are peptides, proteins, antibodies,enzymes, enzyme substrates, nonpolymeric organic compounds, ligands,hormones, receptors, antigens, haptens, lectins, carbohydrates,oligosaccharides, polysaccharides, oligonucleotides, polynucleotides,lipids, lipoproteins, glycoproteins, and proteoglycans.

As discussed above, methods utilizing a primer, template, polymerase andlabeled NTPs or analogs can be used to prepare a branched multisignallabeling reagent, where more than one extended oligonucleotide withlabels are bound to a polymer, as illustrated in FIG. 1, and exemplifiedin Example 19. These methods comprise

-   -   (a) obtaining        -   (i) a primer comprising an oligonucleotide;        -   (ii) a template comprising a nucleic acid comprising a first            sequence that is complementary to the oligonucleotide and a            second sequence that extends in the 5′ direction from the            first sequence;        -   (iii) a polymerase capable of extending the oligonucleotide            along the template nucleic acid when the template nucleic            acid is hybridized to the oligonucleotide at the first            sequence;        -   (iv) nucleotide triphosphates (NTPs) or analogs thereof that            are capable of being incorporated into the extended            oligonucleotide, wherein at least one of the NTPs or analogs            comprises a non-radioactive detectable label, a second            reactive group or a first partner of a second binding pair;            and        -   (v) a polymer capable of binding to more than one of the            extended oligonucleotide, wherein the polymer comprises a            first reactive group or a first partner of a first binding            pair;    -   (b) combining the primer, template, polymerase and NTPs or        analogs under conditions such that the oligonucleotide        hybridizes to the first sequence and is extended along the        second sequence, where the extended oligonucleotide comprises at        least two NTPs or analogs incorporated therein that comprise a        non-radioactive detectable label, a second reactive group or a        first partner of a second binding pair; and    -   (c) combining the extended oligonucleotide with the polymer        under conditions such that at least two of the extended        oligonucleotides bind to the polymer,    -   wherein,        -   (A) if at least one of the two or more NTPs or analogs            incorporated into the extended oligonucleotide comprises a            second reactive group, the method further comprises            combining the extended oligonucleotide with a first compound            comprising a non-radioactive detectable label covalently            linked to a moiety capable of reacting with the second            reactive group such that the label is covalently linked to            the extended primer, and        -   (B) if at least one of the two or more NTPs or analogs            incorporated into the extended oligonucleotide comprises a            first partner of the second binding pair, the method further            comprises combining the extended primer with a second            compound comprising the non-radioactive detectable label            covalently linked to a second binding partner of the second            binding pair.

This method can utilize any non-radioactive label now known or laterdiscovered. Examples of useful non-radioactive detectable labels arefluorophores, phosphorescent moieties, chemiluminescent moieties,chelating moieties, electron dense moieties, magnetic moieties, orenergy transfer moieties.

In some embodiments, the non-radioactive detectable labels arefluorophores, e.g., symmetric or asymmetric cyanines, merocyanines,styryl moieties, oxazines, xanthenes, coumarins or iminocoumarins, asdetailed above. In other embodiments, the non-radioactive detectablelabels are chemiluminescent or phosphorescent moieties, as discussedabove.

The oligonucleotide of the multisignaling labeling reagent produced bythis method can be comprised of any form of oligonucleotide or analogthat can be extended with a polymerase, including DNA, RNA, or analogsthereof. Additionally, the oligonucleotide can be of any length, forexample less than 10 nucleotides, less than 20 nucleotides, less than 50nucleotides, less than 100 nucleotides, or 100 or more nucleotides.Further, any polymerase can be used in these methods, provided thepolymerase is capable of extending the primer along the templateoligonucleotide.

In this method, the NTPs or analogs that are labeled with the label,second reactive group, or first binding partner of a second binding pairis preferably only one of the four NTPs or analogs used to extend theprimer, as discussed above in relation to the previously describedmethod.

The at least two NTPs or analogs that are labeled on the extendedoligonucleotide of the multisignal labeling reagent can be incorporatedinto the oligonucleotide as NTPs or analogs comprising the detectablelabels or with the second reactive group or the first binding partner ofthe second binding pair.

Where NTPs or analogs comprising the second reactive group are utilized,the detectable label must subsequently be added by adding a compoundcomprising the non-radioactive detectable label covalently linked to amoiety capable of reacting with the second reactive group such that thelabel is covalently linked to the extended primer, as indicated in step(A) of the method. Examples of reactive groups are discussed above.

In some embodiments, each reactive group is connected to the NTPs oranalogs by a linker arm, also as described above.

Where NTPs or analogs comprising the first binding partner of the secondbinding pair are utilized, the detectable label must subsequently beadded by combining the extended primer with a compound comprising thenon-radioactive detectable label covalently linked to a second bindingpartner of the second binding pair, as indicated in step (B) of themethod. Binding pairs are further discussed above.

In some embodiments, each first binding partner of the second bindingpair is connected to the NTPs by a linker arm.

As discussed above in relation to other multisignal labeling reagents,the multisignal labeling reagents described here can comprise anon-inherent charged group that increases the aqueous solubility of thereagent. Nonlimiting examples of such charged groups include phosphate,carboxylic acid, sulfone, amine and hydroxy groups.

The polymer can be any compound to which more than one oligonucleotide(extended primer) can be bound covalently or noncovalently. Nonlimitingexamples include oligopeptides, proteins, nucleic acids or analogs suchas an oligonucleotide or a polynucleotide, a lipid, a oligosaccharide, apolysaccharide, or a synthetic compound such as an organic polymer(e.g., a plastic). In some embodiments, the polymer is a nucleic acid oranalog and the two or more oligomers are bound to the polymer bycomplementary hybridization. In these embodiments, the polymer can be ofany length, for example less than 10 nucleotides, less than 20nucleotides, less than 50 nucleotides, less than 100 nucleotides, or 100or more nucleotides.

As discussed above, the polymer comprises a first reactive group or afirst partner of a first binding pair, to attach the multisignallabeling reagent to a target. Any reactive group as discussed above maybe utilized here. Where the polymer comprises a first partner of a firstbinding pair, any binding pair, now known or later discovered, may beprovided with the polymer. Examples include a ligand/receptor, ahormone/receptor, biotin/avidin, biotin/streptavidin and anantigen/antibody. A preferred first partner of a first binding pair isbiotin. See, e.g., Example 19.

For its ultimate use, these methods can further comprise combining themultisignal labeling reagent with a target molecule such that themultisignal labeling reagent is bound to the target by the firstreactive group or the first partner of the first binding pair. Thetarget may be any compound to which a detectable label is desired.Nonlimiting examples of targets are peptides, proteins, antibodies,enzymes, enzyme substrates, nonpolymeric organic compounds, ligands,hormones, receptors, antigens, haptens, lectins, carbohydrates,oligosaccharides, polysaccharides, oligonucleotides, polynucleotides,lipids, lipoproteins, glycoproteins, and proteoglycans.

Preferred embodiments are described in the following examples. Otherembodiments within the scope of the claims herein will be apparent toone skilled in the art from consideration of the specification orpractice of the invention as disclosed herein. It is intended that thespecification, together with the examples, be considered exemplary only,with the scope and spirit of the invention being indicated by theclaims, which follow the examples.

Example 1. Multisignal Labeling Reagent

a) a 33-mer oligonucleotide with the following structure is synthesized:

(SEQ ID NO: 1) 5′-PO₄-T TU* T T T TT U* T T T T T U* T T T T TU*T T T T T U* T T T T T U*-3′where the 5′ end has a phosphate group and the oligonucleotide comprisesallylamine modified Uridine moieties (symbolized as U*).

b) The active ester of tetramethyl rhodamine (TAMRA), rhodamine 110, orthe aphenylic Texas Red analogue described in U.S. Pat. No. 7,166,478,can be reacted with the allylamine moieties in the oligonucleotide toproduce a labeled oligonucleotide using the same procedures described inthat reference for attachment of the TAMRA, rhodamine 110, or aphenylicTexas Red analogue to allylamine modified dUTP.

c) The 5′ phosphate of the labeled oligonucleotide is reacted with aprimary dialkylamine by the procedure described by Halloran and Parker(1966, J. Immunol 96:373) thereby transforming the labeledoligonucleotide into a multisignal labeling reagent with a 5′ aminegroup.

d) The primary amine at the 5′ end is then reacted with a 20 fold molarexcess of succinylmaleic acid active ester at pH 7.8 for 45 minutes atroom temperature to tether the maleimide group to the 5′ end. The pH isimmediately adjusted to pH 4-5 by adding concentrated acetic acid andthe maleimide derivatized oligonucleotide is precipitated by ethanol. Itis then resuspended in LiAc (pH 4) buffer and precipitated again. Beforeuse, the maleimide derivatized oligonucleotide is dissolved in Acetatebuffer (pH 5.5). This procedure generates a multisignal labeling reagentthat comprises 6 TAMRA, rhodamine 110, or Texas Red dye moieties and asingle reactive group for attachment to a desirable target.

Example 2. Use of Multisignal Labeling Reagent with Proteins

The reagent from Example 1 can be used directly to label a protein thathas available sulfhydryl groups. For instance, BSA can be labeled atroom temperature by reacting it with the maleimide derivatized reagentat pH 5.5.

Example 3. Modification of Proteins for Use with Multisignal LabelingReagent

Proteins that lack available sulfhydryl groups may also be used with thereagent from Example 1. For instance, an antibody can be treated withN-acetyl-homocysteine thiolactone at pH 9 thereby introducing sulfhydrylgroups that can be labeled with the maleimide derivatized reagent asdescribed above in Example 2. By varying the reaction time andconcentration of the N-acetyl-homocysteine thiolactone, the number ofsulfhydryl groups introduced into a protein can be controlled. To retainbiological activity, it is preferred that an antibody be modified withat most 2-3 sulfhydryl groups.

Example 4. Modification of Multisignal Labeling Reagent

The multisignal labeling reagent described in step c) of Example 1 istreated with bromoacetic acid NHS ester to tether a bromoacetyl group tothe 5′ end. This group is very reactionary to primary amines and can beused at pH 9 to label a protein or other desirable group that containsprimary amines or thiol groups. As described previously, these groupscan be native to the target molecule or introduced.

Example 5. Multisignal Labeling Reagent Used with Glycoprotein

In addition to the amine and sulfhydryl groups described previously,many proteins that are isolated from mammalian cells are gycosylated,thereby providing an additional target group that can be used forattachment. A notable example of such proteins are antibodies. Oxidationof IgG can be carried out in the dark at 4° C. for 20 minutes with 10 mMperiodate at pH 4-5 to introduce aldehyde groups into the antibody. Theexcess periodate is removed afterwards by G50 fractionation. Amodification reagent is prepared by reacting cystathione with Elman'sReagent thus blocking the thiol moiety with a removable group. Thealdehyde groups on the glycon portion of the antibody are then reactedwith a 40 fold excess of the modification reagent at pH 6 for one hourat room temperature. The pH is then raised to pH 9, the solution iscooled and the Schiff's base is reduced with NaBH₄. This reduces theSchiff's base to an amine and liberates the thiol. The excess NaBH₄ isdestroyed by adding acetate buffer (pH 4). The thiol labeled IgG is nowavailable for linkage with the either the maleimide dervatized reagentfrom Example 1 or the bromoacetyl modified reagent from Example 4. Itshould be noted that this method results in a very controlled extent oflabeling since it only takes place on sites where gycosylation has takenplace. For example, the antibody used in this example is glycosylated inthe constant region. As such, attachment of the labeling reagent shouldnot interfere with the variable region, the part of the antibody that isresponsible for the binding of the antibody to its antigen target.

Example 6. Multisignal Reagent with a Reactive Group at the 3′ End

A 29-mer oligonucleotide with the following structure is synthesized;

(SEQ ID NO: 2)5′-U^(F) T T T T T T U^(F) T T T T T T U^(F) T T T T T T U^(F)T T T T T T U^(F)-NH₂-3′where the oligonucleotide comprises a 3′ primary amine and uridines thathave fluorescein labels (symbolized by U^(F)). Phosphoramidites and CPGfor making an oligonucleotide with these modification are commerciallyavailable. Alternatively, a phosphoramidite for synthesis of anoligonucleotide with a primary amine in the 5′ end could have been usedto synthesize a similar labeled oligonucleotide. This product comprises5 fluorescein moieties and a single amine group. This reagent may beused with the same processes described previously for Examples 1, 2, 3,4 and 5.

Example 7. Use of Terminal Transferase to Synthesize a MultisignalLabeling Reagent

a) A 27-mer oligonucleotide with the following structure is synthesized;

SEQ ID NO: 3 5′-U* T T T T T U* T T T T T U* T T T T T U*T T T T T U*T T-3′where the oligonucleotide comprises allylamine modified uridines(symbolized by U*). Attachment of the active ester of Alexa Fluor 555(Molecular Probes, Inc, Eugene, Oreg.) can be carried out by the methodspreviously described in Example 1.

b) The labeled oligonucleotide can be further reacted by the addition ofa dideoxy version of allylamine dUTP by terminal transferase. This stepwill introduce a single amine group into the 3′ end of theoligonucleotide, thereby creating a labeling regent with 5 Alexa dyesand a single amine group. This labeling reagent can then be used asdescribed previously.

Example 8. Synthesis of Multisignal Labeling Reagent Using Mercuration

A 57-mer oligonucleotide with the following structure is synthesized:

SEQ ID NO: 4 5′ (U T T T T T T)₈ T-NH₂-3′where the 3′ end has an amine group. The oligonucleotide is treated witha 3 fold molar access of mercuric acetate in acetate buffer (ph 4.0) for5 hours at 65° C. to mercurate the 5 position of the uridine ring of theoligonucleotides. The mercurated oligonucleotides are then precipitatedwith ethanol and kept at −20° C. until needed. The oligonucleotide isthen reacted with a Cy dye that comprises a terminal double bondreactive group as described in U.S. Pat. No. 7,166,478. The resultantoligonucleotide should then comprise a single amine reactive group atthe 3′ end and a Cy dye at each of the 8 sites where there was a U. Thislabeling reagent may then be used as described above.

Example 9. Protein Labeled by Means of Two Strands of Nucleic Acid

a) A 12-mer oligonucleotide with the following structure is synthesized;

(SEQ ID NO: 5) 5′-GTG U* GTG U* GTG U*-3′where the oligonucleotide comprises allylamine modified uridines(symbolized by U*).

b) The active ester of the TAMRA, rhodamine 110, or aphenylic Texas Redanalogue used in Example 1 can be reacted with the allylamine moietiesin the oligonucleotide to produce a Signal Oligonucleotide using thesame procedures described above.

c) A 50-mer Attachment Oligonucleotide with the following structure issynthesized;

(SEQ ID NO: 6) 5′-(A C)₂₅-NH₂-3′

d) The TAMRA, rhodamine 110, or Texas Red labeled signal oligonucleotideis annealed to the attachment oligonucleotide to form a multisignallabeling reagent. Due to the redundancy of the dinucleotide repeats,hybridization should enjoy fast kinetics. The signal oligonucleotidesare smaller than the attachment oligonucleotide such that there issufficient room for as many as 4 dignal oligonucleotides to bind to eachattachment oligonucleotide of the multisignal labeling reagent. Thiswould result in 12 signal moieties potentially being attached to everysite on a target that is linked through the amine group of themultisignal labeling reagent. Using the 2° C. per A/T base-pair and 4°C. per G/C base-pair rule, the theoretical T_(m) of the signaloligonucleotides should be about 36° C. As such, the multisignallabeling reagent complexes should be quite stable at room temperature.Even higher T_(m)s will probably be realized since hybridization of twosignal oligonucleotides on adjacent sites of the attachmentoligonucleotide should allow stacking interactions that will favor thethermal stability of each oligonucleotide.

e) The multisignal labeling reagent can be attached to a protein throughthe amine group as described previously to form a labeled proteincomprising multiple signals at each attachment site on the protein.

Example 10. Preparation of Samples for a Protein Array

a) A 15-mer oligonucleotide with the following structure is synthesized;

(SEQ ID NO: 7) 5′-TGCU* GCTG CU GC U*GC-3′where the oligonucleotide comprises allylamine modified uridines(symbolized by U*)

b) The active ester of the TAMRA, rhodamine 110, or aphenylic Texas Redanalogue is reacted with the allylamine moieties in the oligonucleotideto produce Signal Oligonucleotide #1 by the methods described previouslyin Example 1. The T_(m) of this oligonucleotide should be about 50° C.

c) Attachment Oligonucleotide #1 (a 63-mer) with the following structureis synthesized;

(SEQ ID NO: 8) 5′-(GCA)₂₁-NH₂-3′

d) Signal Oligonucleotide #1 is annealed to Attachment Oligonucleotide#2 to form Multisignal Labeling Reagent #1 which at saturation valuesshould have 8 TAMRA, rhodamine 110, or Texas Red moieties bound per 3′NH₂ group.

e) A 15-mer oligonucleotide with the following structure is synthesized;

(SEQ ID NO: 9) 5′-TCGU* CGTCGUCG U*CG-3′where the oligonucleotide comprises allylamine modified uridines(symbolized by U*).

f) Using the same methods as in step (b), the active ester of AlexaFluor 647 (Molecular Probes, Inc, Eugene, Oreg.) is reacted with theallylamine moieties in the oligonucleotide to produce MultisignalOligonucleotide #2. The T_(m) of this oligonucleotide should also beabout 50° C.

g) Attachment Oligonucleotide #2 (a 63-mer) with the following structureis synthesized;

(SEQ ID NO: 10) 5′-(CGA)₂₁-NH₂-3′

h) Signal Oligonucleotide #2 is annealed to Attachment Oligonucleotide#2 to form Multisignal Labeling Reagent #2 which at saturation valuesshould have 8 Alexa moieties bound per 3′ NH₂ group.

i) Protein sample #1 is reacted with Multisignal Labeling Reagent #1from step (d) and Protein sample #2 is reacted with Multisignal LabelingReagent #2 from step (d) using any of the methods described in theprevious examples.

These samples are now ready to be applied to a protein array wheresignals from protein sample #1 (TAMRA, rhodamine 110, or Texas Red) willbe distinguishable from signals from Protein sample #2 (Alexa). Asdescribed above, linkage of a multisignal labeling reagent of thisExample of the present invention should allow joining as many as 8× theamount of signal moieties as would result from using a single dye withan amino group.

Example 11. Multisignal Labeling Reagent with Single-Stranded Tails

a) A 50-mer attachment oligonucleotide with the following structure issynthesized;

(SEQ ID NO: 6) 5′-(A C)₂₅-NH₂-3′

b) A 32-mer signal oligonucleotide with the following structure issynthesized;

(SEQ ID NO: 11) 5′-GTG U* GTG U* GTG U* G TG U* T T TU* T T TU*T T TU* T T TU*-3′where the oligonucleotide comprises allylamine modified uridines(symbolized by U*)

c) The active ester of the TAMRA, rhodamine 110, or aphenylic Texas Redanalogue is reacted with the allylamine moieties in the oligonucleotideto produce a tailed signal oligonucleotide. The 16 base segment at the5′ end of the signal oligonucleotide is complementary to the attachmentoligonucleotide of step (a) and should have a T_(m) of about 48° C.based on 8 G's and 8 T/U's. The 16 base 3′ tail segment of the signaloligonucleotide consisting of T's and U*'s should contribute signal butshould not participate in binding to the attachment oligonucleotide.

d) Hybridization of the signal oligonucleotides to the attachmentoligonucleotide forms a multisignal labeling reagent that could provideas many as three signal oligonucleotides, each having 8 signal moieties,for a net total of 24 signal moieties potentially bound to each sitewhere the attachment oligonucleotide portion of the multisignal labelingreagent will be linked to the protein target.

The unlabeled attachment oligonucleotide portion of the multisignalreagent is used for linkage to a protein through the amine group asdescribed previously to form a labeled target comprising one or moremultisignal labeling reagents.

Example 12. Double-Stranded Multisignal Labeling Reagent with Biotin asa Binding Partner

a) A 50-mer biotinylated attachment oligonucleotide with the followingstructure is synthesized;

(SEQ ID NO: 6) 5′-(A C)₂₅-biotin dU-3′Phosphoramidites for a 3′ biotin labeled nucleotide are readilyavailable from numerous commercial sources.

b) The tailed signal oligonucleotides from step (c) of Example 9 arehybridized to the biotinylated attachment oligonucleotide to form abiotinylated multisignal labeling reagent. As described previously, thiscomplex could comprise as many as 24 signal moieties with only a singlebiotin attachment moiety.

c) Biotinylated antibodies are readily available from a number ofcommercial sources. A biotinylated antibody can be can be bound toappropriate target antigens in a tissue section specimen and amplifieddetection of the presence of antigens can be carried out by firstbinding streptavidin followed by signal generation through binding ofthe Biotinylated Multisignal Labeling Reagent from step (b).

Example 13. Single-Stranded Multisignal Reagent with Biotin as a BindingPartner and Addition of Noise Suppressor

a) a 61-mer oligonucleotide with the following structure is synthesized:

(SEQ ID NO: 12) 5′-BiotinU-(U*G T G T G T G T G T G)₅-3′where the 5′ end has a biotinylated U and the oligonucleotide comprisesallylamine modified uridine moieties (symbolized as U*)

b) The active ester of Cy 3 dye (Amersham Biosciences, Piscataway, N.J.)can be reacted with the allylamine moieties in the oligonucleotide usingthe same procedures described above. To form a Cy3 labeled biotinylatedmultisignal labeling reagent:

c) a 20-mer oligonucleotide with the following sequence is synthesized:

(SEQ ID NO: 13) 5′-(TG)₁₀-3′without labels or biotin to provide a noise suppressor.

d) PolyA mRNA is amplified according to the procedure described in USPatent Publication 2004/0161741, describing biotin incorporation duringin vitro transcription of the double-stranded cDNA collection to producelabeled anti-sense RNA.

e) The biotinylated RNA is fragmented and hybridized to a High Densitymicroarray chip form Affymetrix according to the manufacturer'sinstructions (Affymetrix, Inc. Santa Clara, Calif.).

e) The chips are incubated with strepavidin according to the Affymetrixinstructions.

f) Instead of using biotinylated phycoerythrin as described in theAffymetrix instructions, the chip is incubated with a mixture of the Cy3labeled biotinylated multisignal labeling reagent from step (b) and thenoise suppressor from step (c).

g) After appropriate washing, signal generation from each locus is thenmeasured.

Example 14. Single-Stranded Multisignal Labeling Reagent with Biotin asa Binding Partner and Addition of Unlabeled Complement

a) a 61-mer oligonucleotide with the following structure is synthesized:

(SEQ ID NO. 12) 5′-BiotinU-(U* G T G T G T G T G T G)₅-3′where the 5′ end has a biotinylated U and the oligonucleotide comprisesallylamine modified uridine moieties (symbolized as U*).

b) The active ester of Cy 3 dye (Amersham Biosciences, Piscataway, N.J.)can be reacted with the allylamine moieties in the oligonucleotide usingthe same procedures described above. To form a Cy3 labeled biotinylatedmultisignal labeling reagent.

c) A 20-mer oligonucleotide with the following structure is synthesized:

(SEQ ID NO: 14) 5′-(AC)₁₀-3′without labels or biotin to provide a multisignal labeling reagentcomplement. The T_(m) of this oligonucleotide should be about 60° C.based on 10 C's and 10 A's.

d) Poly A mRNA is amplified according to the procedure described in U.S.Pat. No. 7,166,478, where biotin is incorporated during in vitrotranscription of the double-stranded cDNA collection to produce labeledanti-sense RNA.

e) The biotinylated RNA is fragmented and hybridized to a high densitymicroarray chip from Affymetrix according to the manufacturer'sinstructions (Affymetrix, Inc., Santa Clara, Calif.).

e) The chips are incubated with strepavidin according to the Affymetrixinstructions.

f) Instead of using biotinylated phycoerythrin as described in theAffymetrix instructions, the chip is incubated with a mixture of the Cy3labeled biotinylated multisignal labeling reagent from step (b) and themultisignal reagent complement from step (c). Hybridization of themultisignal reagent complement to the Cy3 labeled biotinylatedmultisignal labeling reagent can take place during this step or ifdesired they can be preincubated together prior to application to thechip. By endowing the Cy3 labeled biotinylated multisignal labelingreagent with double-stranded character, quenching caused by interactionsof the Cy 3 moities could be reduced. Also if desired, the noisesuppressor from step (c) of Example 11 may be included.

g) After appropriate washing, signal generation from each locus is thenmeasured.

Example 15. Multisignal Labeling Reagent with Biotin and Energy Transfer

a) a 61-mer oligonucleotide with the following structure is synthesized:

(SEQ ID NO: 15) 5′-Biotin U-(C^(F) A C A C A C A C A C A)₅-3′where the 5′ end has a biotinylated U and the oligonucleotide comprisesfluorescein modified cytidine moieties (symbolized as C^(F)) to form anenergy donor multisignal labeling reagent.

b) a 20-mer oligonucleotide with the following structure is synthesized:

(SEQ ID NO: 16) 5′-T G T G U* G T G T G T G T G U* G T G T G-3′where the 5′ end has a biotinylated U and the oligonucleotide comprisesallylamine modified uridine moieties (symbolized as U*). The T_(m) ofthis oligonucleotide should be about 60° C. based on 10 G's and 10T/U's.

c) The active ester of TAMRA, rhodamine 110, or aphenylic Texas Red canbe reacted with the allylamine moieties in the oligonucleotide using thesame procedures described above to form an energy acceptor multisignallabeling reagent.

d) The energy donor multisignal labeling reagent from step (a) and theenergy acceptor multisignal labeling reagent from step (c) arehybridized together to form an energy transfer multisignal labelingreagent which comprises a single biotin and as many as 5 donors and 6acceptors.

e) The energy transfer multisignal labeling reagent can then be used asdescribed above.

Example 16. Synthesis of Streptavidin-Oligonucleotide Bioconjugates

Protocol for Making Streptavidin-Oligo-22Mer Bioconjugates

a) Preparation of Formylbenzoic Acid-Tagged Oligonucleotide(FB-Oligonucleotide)

To a solution of 5′-amino-oligo22mer having the sequence[amino-C6]TTGCTGAGGT CATGGATCGA GA (SEQ ID NO:17) (Eurofins, 30 nmole),in a buffer containing 100 mM phosphate and 150 mM NaCl, pH 7.4, 600nmole of 4-formylbenzoic acid NETS-ester in DMF was added. The mixturewas incubated at room temperature for 2 h and the labeledoligonucleotide, FB-oligonucleotide, was desalted using a 5 k MWCOVivaSpin diafiltration apparatus. FB-oligonucleotide concentration wasdetermined spectroscopically at 260 nm.

b) Preparation of HyNic-Tagged Streptavidin (HyNic-STV)

Streptavidin (Thermo) was desalted into the buffer described under a)above using a Zeba Spin Column. The acetonide of 2-hydrazinoisonicotinicacid NETS-ester (200 nmole) in DMF was then added to 20 nmole of thedesalted streptavidin. The reaction mixture was incubated at roomtemperature for 1.5 h and the labeled protein, HyNic-STV, was desaltedinto the above buffer, pH 6.0 using a 30 k Amicon diafiltration device.HyNic-STV concentration was measured spectroscopically at 280 nm and themolecular substitution ratio (MSR) was determined with2-sulfo-benzaldehyde reagent.

c) Conjugation of HyNic-STV with FB-Oligonucleotide—1:1 STV:Oligo MolarRatio

Desalted HyNic-STV (16.7 nmole) described in b) above was mixed withFB-oligonucleotide (30 nmole) prepared as described in a) above in theabove-described buffer, pH 6.0, along with 100 mM aniline as a catalyst.The reaction mixture was incubated at room temperature for 2 h and thebioconjugate was desalted using a 30 k Amicon diafiltration device. TheSTV-Oligonucleotide bioconjugate concentration was measuredspectroscopically at 354 nm and the purity was determined by 4-16%native gel polyacrylamide electrophoresis followed by sequentialstaining with ethidium bromide and Coomassie stain.

d) Conjugation of HyNic-STV with FB-Oligonucleotide—1:2 STV:Oligo MolarRatio

Desalted HyNic-STV (10 nmole) was mixed with FB-oligonucleotide (25nmole) in the above-described buffer, pH 6.0, along with 100 mM anilineas a catalyst. The reaction mixture was incubated at room temperaturefor 2 h and the bioconjugate was desalted using a 30 k Amicondiafiltration device. STV-oligonucleotide bioconjugate concentration wasmeasured spectroscopically at 354 nm and the purity was determined by4-16% native gel polyacrylamide electrophoresis followed by sequentialstaining with ethidium bromide and Coomassie stain.

Protocol for Making Streptavidin-Oligo-60Mer Bioconjugate

a) Preparation of Formylbenzoic Acid-Tagged Oligonucleotide(FB-Oligonucleotide)

To a solution of 5-amino-oligo60mer having the sequence[amino-C6]TTTTGACACG GGTCCTATGC CTTGACACGG GTCCTATGCC TTGACACGGGTCCTATGCCT (SEQ ID NO:18) (Eurofins, 10 nmole) in the above-describedbuffer, pH 7.4, 200 nmole of 4-formylbenzoic acid NETS-ester in DMF wasadded. The mixture was incubated at room temperature for 2 h and thelabeled oligonucleotide, FB-oligonucleotide, was desalted using a 5 kMWCO VivaSpin diafiltration apparatus. FB-oligonucleotide concentrationwas determined spectroscopically at 260 nm.

b) Preparation of NyNic-Tagged Streptavidin (HyNic-STV)

Streptavidin (Thermo) was desalted into the buffer described above usingZeba Spin Column. To 10 nmole of this desalted streptavidin in the abovebuffer, 100 nmole of the acetonide of 2-hydrazinoisonicotinic acidNETS-ester in DMF was added. The reaction mixture was incubated at roomtemperature for 1.5 h and the labeled protein, HyNic-STV, was desaltedinto the above-described buffer, pH 6.0 using a 30 k Amicondiafiltration device. HyNic-STV concentration was measuredspectroscopically at 280 nm while the molecular substitution ratio (MSR)was determined with 2-sulfo-benzaldehyde reagent.

c) Conjugation of HyNic-STV with FB-Oligonucleotide

Desalted HyNic-STV (6 nmole) described in b) above was mixed withFB-oligonucleotide (10 nmole) prepared as described in a) above in theabove-described buffer, pH 6.0, along with 100 mM aniline as a catalyst.The reaction mixture was incubated at room temperature for 2 h and thebioconjugate was desalted using 30 k Amicon diafiltration device. TheSTV-oligonucleotide bioconjugate concentration was measuredspectroscopically at 354 nm and the purity was determined by 4-16%Native gel polyacrylamide electrophoresis followed by sequentialstaining with SYBR Gold and Coomassie stain.

Example 17. Synthesis of Alkaline Phosphatase-Oligo-20Mer Bioconjugates

Note: Two oligo-20mers, one containing biotin (control) and one withoutbiotin (probe), were prepared in parallel. Otherwise the sequences ofboth oligomers were identical.

a) Preparation of Labeled Oligonucleotides (FB-Oligonucleotide)

20NoBiotinAminoC6—Alkaline Phosphatase-Oligonucleotide Bioconjugate (theprobe):

(SEQ ID NO: 19) [AminoC6]TTTTAGCTTTTCAGTTTTGACTA

20BiotinAminoC6—the control for Alkaline Phosphatase-OligonucleotideBioconjugate:

(SEQ ID NO: 19) [AminoC6]TTTTAGCTTTTCAGTTTTGACTA + biotin  (on 3′ end)

To 1 mM solution of 5′-amino-oligo20mers (Eurofins, 50 nmole) in abuffer containing 100 mM phosphate and 150 mM NaCl at pH 7.4, 20 molarequivalents (1.0 μmole) of 4-formylbenzoic acid NETS-ester (Solulink) inDMF was added. The mixture was incubated at room temperature for 2 h andthe labeled oligonucleotides, FB-oligonucleotides, were desalted using 3k Amicon diafiltration devices (14,000×g, 20 min). FB-Oligonucleotideconcentration was determined spectroscopically at 260 nm.

b) Preparation of Labeled Alkaline Phosphatase (HyNic-AP)

Alkaline phosphatase (Thermo) was desalted into the buffer described ina) above using Zeba Spin Column. Then, to 70 nmole of desalted proteinin the above buffer, 20 molar equivalents (1.4 μmole) of the acetonideof 2-hydrazinoisonicotinic acid NETS-ester (Solulink) in DMF was added.The reaction mixture was incubated at room temperature for 1.5 h and thelabeled protein, HyNic-AP, was desalted into the above-described buffer,pH 6.0 using a 30 k Amicon diafiltration device. HyNic-AP concentrationwas measured spectroscopically at 280 nm while the molecularsubstitution ratio (MSR) was determined with 2-sulfobenzaldehyde reagent(Solulink).

c) Conjugation of HyNic-AP with FB-Oligonucleotides

Desalted HyNic-AP (28 nmole) described in b) above was mixed with eachof the FB-oligonucleotides (50 nmole) prepared as described in b) abovein the above-described buffer, pH 6.0, along with and 100 mM aniline asa catalyst. The reaction mixtures were incubated at room temperature for2 h and the bioconjugates were desalted using 30 k Amicon diafiltrationdevices. AP-oligonucleotide bioconjugate concentration was measuredspectroscopically at 354 nm and the purity was determined by 4-16%native gel polyacrylamide electrophoresis followed by sequentialstaining with ethidium bromide and Coomassie stain.

Example 18. Adding Multiple Labels to a Single Reporter Molecule UsingDNA Polymerase

A short oligonucleotide with the sequence 5′-C6 amino-TTGCTGAGGTCATGGATCGA GA-3′ (SEQ ID NO:17) is attached to streptavidin as describedin Example 16, using the protein oligo conjugation kit (Solulink, SanDiego, Calif., catalog #S-9011-1). The streptavidin oligo conjugate ismixed with a template oligo of the sequence 5′-ACTTCTACTT CTACTTCTACTTCTACTTCT ACTTCTACTT CTACTTCTAC TCTTACTCTT ACTCTTCATT GGTCATCTCGATCCATGACC TCAGC-3′. (SEQ ID NO:20)

172 pMol of the streptavidin oligo construct is incubated with 200 pMolof template oligo in 50 mM NaCl, 10 mM Tris-HCl, 10 mM MgCl₂, 1 mMdithiothreitol, pH 7.9, 5 nMol rhodamine-dUTP (fluorescein dUTP has alsobeen used successfully), 15 nMol each dATP, dCTP and dGTP and 6 units ofE. coli DNA polymerase I Klenow fragment exo⁻ (New England Biolabs,Ipswich, Mass.) in a total volume of 20 μl at 37° C. for 2 hours. Theextension reaction was stopped with 2 μl of 500 mM EDTA, and theunincorporated nucleotides are removed using NucAway spin columns(Applied Biosystems/Ambion, Austin, Tex.) as described by themanufacturer. FIG. 2 is a diagram of this procedure.

A model system for in situ hybridization is HPV16/18 integration intothe chromosome of different cell lines. HeLa cells have 30-50 copies ofHPV18 integrated into its chromosome and SiHa cells have 1-5 chromosomalcopies of HPV16 (Schwarz et al., 1995, Nature 314:111-114; Micheva etal., 1987, Med Microbiol Immunol 176:245-256). The cells HeLa, SiHa andthe HPV negative control SK—N—SH (ATCC, Manassas, Va.) were grown onslides at a density of about 10⁵ cells/ml. After growth overnight inEagle's Minimum Essential Medium supplemented with 10% fetal bovineserum (FBS, ATCC) and 100 u/ml penicillin with 100 μg/ml streptomycin(Sigma-Aldrich, St. Louis, Mo.) at 37° C., 5% CO₂ in a humidifiedchamber, the cells were washed for 5 minutes in PBS, then fixed in 100%Acetone for 5 minutes, followed by air drying. The slides were treatedin 10 mM sodium citrate at 80° C. for 1 hour, then washed in 2×SSC(Sambrook and Russell, 2001, Molecular Cloning: A Laboratory Manual.Cold Spring Harbor, N.Y., CSHL Press) for 5 minutes. DNA was denaturedat 73° C. for 5 minutes in 70% formamide, 2×SSC, followed by 70% ethanolfor 1 minute, 90% ethanol 1 minute and 100% ethanol for 1 minutefollowed by drying at 37° C. for 2 minutes. 12 μl of HPV16/18biotinylated DNA probe (ENZO Life Sciences, Farmingdale, N.Y.) was addedto each well of cells, and then a coverslip was added and sealed withrubber cement. The probe was denatured at 80° C. for 5 minutes, and thenhybridization was performed overnight at 37° C. in a humidified chamber.The following day, the coverslip was removed and the slide was washed inPBS for 5 minutes, then in 40% formamide, 6×SSPE (Id.) at 37° C. for 10minutes. The slide was again washed with PBS, then with Superblock inTBS (Thermo Scientific, Rockford, Ill.) for 15 minutes. Detection wasachieved by incubation of 30 nM labeled streptavidin in Superblock inTBS containing 200 μg/ml single-stranded salmon sperm DNA (80 μl perwell) at room temperature in the dark for 1 hour. This was washed withPBS for 1 minute, and then incubated with PBS containing 0.5 Hoechst33342 for 15 minutes at room temperature for a nuclear counter stain.Two washes in PBS removed excess dye. The wells were kept moist withPBS, and a coverslip was added for visualization. Cells were observedusing a fluorescence microscope (Carl Zeiss Microlmaging GmbH, Jena,Germany) equipped with a Texas Red filter set for rhodamine, a DAPIfilter set for Hoechst and a FITC filter set for fluorescein. Imageswere acquired with a 63× objective lens (Carl Zeiss, Inc).

FIG. 3 shows that streptavidin with the extended oligos (13 rhodamines)can detect 1 to 5 copies of HPV16 in SiHa cells with very littlebackground in control cells (SK—N—SH) lacking HPV16. In these conditionsplain rhodamine, streptavidin or phycoerythrin streptavidin (LifeTechnologies, Eugene, Oreg.) failed to detect the HPV16 in SiHa cells(data not shown). The inability of phycoerythrin streptavidin to detectthe HPV may be due to the large size of the fluorescent moleculepreventing access to the biotinylated probe DNA.

Example 19 Combining Extended Oligo with Branched DNA

A multiple rhodamine labeled oligo was created by mixing the followingoligos:

Mext6- (SEQ ID NO: 21)5′-TACTGCTACTGCTACTTCTACTGCTACTGCTACTTCTACTGCTACTCTGACTCTGACTCTTCATTGGTCACTACACCAACAGCATGAC-3′ LPrimS-5′-AGGCATAGGACCCGTGTCTTT[spacer][spacer] GTCATGCTGTTGGTGTAG-3′(SEQ ID NO: 22 and SEQ ID NO: 23, respectively)Where “[spacer]” is a 9 atom chain that has no base and cannot be usedas a template.

LPrimS (8 pmoles) was mixed with 8.8 pmoles Mext6 in the presence of 26nmoles dATP, dCTP and dGTP, and 11.6 nmoles rhodamine-5-dUTP. DNApolymerase I Klenow exo⁻ (5 units) in a buffer containing 50 mM sodiumchloride, 20 mM tris acetate, 10 mM magnesium acetate, 1 mMdithiothreitol and 500 mM trehalose was added to the above mixture andincubated at 46° C. for 1 h. The labeled oligo was purified fromunincorporated nucleotides using NucAway spin columns (AppliedBiosystems, Austin, Tex.) according to the manufacturer's instructions.The 5′ end of LprimS remains single-stranded and free to bind a secondoligonucleotide. Similar labeling of a single end of a primer could beachieved with the use of a 3′ end blocked terminus of the templateoligo.

The branched DNA was produced by mixing 262.5 pmoles of the extendedoligo from above with 50 pmoles of Bio-Linker(5′-biotin-TATGACACGGGTCCTATGCCTTGACACGGGTCCTATGCCTTGACACGGGTCCTATGCCTTGACACGGGTCCTATGCCTTGACACGGGTCCTATGCCT-3′) (SEQ ID NO:24) that has 5binding sites for the single-stranded portion of the extended oligo.This was mixed while stirring at a 1:1 ratio with streptavidin, startingwith 5.9 μM streptavidin and 5.9 μM of the Bio-Linker branch in PBS. Theresulting product should on average have one branched oligo perstreptavidin, leaving two or three biotin binding sights on thestreptavidin free.

The resulting complex was diluted to 10 nM or 5 nM in Superblock in TBS(Thermo Scientific, Rockford, Ill.). The extended oligorhodamine-labeled streptavidin from Example 18 was diluted in a similarmanner to 10 nM and 5 nM. 100 μl of the labeled streptavidin solutionswere used to bind pre-blocked biotin-coated 96 well plates(G-Biosciences, Maryland Heights, Mo.) in duplicate. The streptavidinwas allowed to bind for one hour at room temperature with slow shaking(100 RPM). After binding, the wells were washed 4 times with PBScontaining 0.05% Tween 20. 60 μl PBS was added to each well of theplate, and the plate was read from the top using a BioTek SynergyMX(Winooski, Vt.) at 554 nm excitation and 584 emission using a 9 nm slitwidth for each. The results were as follows:

Oligo-streptavidin Bio-linker/LPrimS mix 10 nM 972 3,440 5 nM 579 2,1690 nM 24 21 10 nM pre-blocked with 25 63 20 μM streptavidinThe binding of the 10 nM streptavidin complexes was eliminated if 20 μMstreptavidin was first bound to the plate before the labeledstreptavidin was added. It can be seen that the signal of the branchedreagent is increased about four fold over the linear reagent. Thisdemonstrates that the extended, branched oligo is functional andspecific.

Example 20. Synthesis of Spermidine-Diacridine (Compound 1)

Heat a mixture of phenol (3.51 g, 37.3 mmol) and 9-chloroacridine (1.6g, 7.46 mmol) in an oil bath at 120° C. for 1 h. To this mixture addspermidine (0.54 g, 0.58 mL, 3.73 mmol) and continue heating for another2.5 h. Pour into 75 mL of 2N NaOH solution and extract with chloroform(2×50 mL). Wash the organic layer with 1N NaOH (1×75 mL), water (2×100mL), brine (2×100 mL) and dry with MgSO₄. Recrystallize the yellow solidthus obtained with ethanol to obtain Compound 1 (30% yield). Thestructure of Compound 1 is given below:

Example 21. Synthesis of Spermidine-6-chloro-2-methoxydiacridine(Compound 2)

The procedure can be carried out as described in Example 20 using6-chloro-2-methoxy acridine, phenol and spermidine. The structure ofCompound 2 is given below:

Example 22. General Procedure for Labeling Dyes to DiacridineDerivatives

Cool (in an ice bath) a solution of dye acid (1 eq.) anddiisopropylethyl amine (3 eq.) in DMF under stirring. AddBromo-tris-pyrrolidino phosphoniumhexafluorophosphate (PyBrop) (1 eq.)and continue stirring in the ice bath for 15 minutes. Add theappropriate diacridine derivative from Example 20 or 21 and continuestirring in the ice bath for another 15 minutes and at room temperaturefor 12 hours. Add a mixture of dichloromethane and water (1:1) to thereaction. Wash the organic layer with water and brine and dry overMgSO₄. Evaporate the solvent and obtain the desired product bypurification on Biotage using a SNAP column. General structure of theconjugate is shown below:

In view of the above, it will be seen that several objectives of theinvention are achieved and other advantages attained.

As various changes could be made in the above methods and compositionswithout departing from the scope of the invention, it is intended thatall matter contained in the above description and shown in theaccompanying drawings shall be interpreted as illustrative and not in alimiting sense.

All references cited in this specification are hereby incorporated byreference. The discussion of the references herein is intended merely tosummarize the assertions made by the authors and no admission is madethat any reference constitutes prior art. Applicants reserve the rightto challenge the accuracy and pertinence of the cited references.

What is claimed is:
 1. A method of producing a multisignal labelingreagent, the method comprising (a) obtaining (i) a primer comprising anoligonucleotide; (ii) a template comprising a nucleic acid comprising afirst sequence that is complementary to the oligonucleotide and a secondsequence that extends in the 5′ direction from the first sequence; (iii)a polymerase capable of extending the oligonucleotide along the templatenucleic acid when the template nucleic acid is hybridized to theoligonucleotide at the first sequence; (iv) nucleotide triphosphates(NTPs) or analogs thereof that are capable of being incorporated intothe extended oligonucleotide, wherein at least one of the NTPs oranalogs comprises a non-radioactive detectable label, a second reactivegroup or a first partner of a second binding pair; and (v) a polymercapable of binding to more than one of the extended oligonucleotide,wherein the polymer comprises a first reactive group or a first partnerof a first binding pair; (b) combining the primer, template, polymeraseand NTPs or analogs under conditions such that the oligonucleotidehybridizes to the first sequence and is extended along the secondsequence, where the extended oligonucleotide comprises at least two NTPsor analogs incorporated therein that comprise a non-radioactivedetectable label, a second reactive group or a first partner of a secondbinding pair; and (c) combining the extended oligonucleotide with thepolymer under conditions such that at least two of the extendedoligonucleotides bind to the polymer, wherein, (A) if at least one ofthe at least two NTPs or analogs incorporated into the extendedoligonucleotide comprises a second reactive group, the method furthercomprises combining the extended oligonucleotide with a first compoundcomprising a non-radioactive detectable label covalently linked to amoiety capable of reacting with the second reactive group such that thelabel is covalently linked to the extended primer, and (B) if at leastone of the at least two NTPs or analogs incorporated into the extendedoligonucleotide comprises a first partner of the second binding pair,the method further comprises combining the extended primer with a secondcompound comprising the non- radioactive detectable label covalentlylinked to a second binding partner of the second binding pair.
 2. Themethod of claim 1, wherein the non-radioactive detectable labels arefluorophores, phosphorescent moieties, chemiluminescent moieties,chelating moieties, electron dense moieties, magnetic moieties, orenergy transfer moieties.
 3. The method of claim 1, wherein thenon-radioactive detectable labels are fluorophores.
 4. The method ofclaim 1, wherein the two NTPs or analogs incorporated into the extendedoligonucleotide are each labeled with a reactive group.
 5. The method ofclaim 4, wherein each reactive group is joined to the NTPs by a linkerarm.
 6. The method of claim 1, wherein the NTP or NTP analogs are eachlabeled with a non-radioactive detectable label.
 7. The method of claim3, wherein the NTP or NTP analogs are each labeled with a first bindingpartner of a second binding pair.
 8. The method of claim 7, wherein thefirst binding partner of the second binding pair is a biotin.
 9. Themethod of claim 7, wherein each first binding partner of the secondbinding pair is connected to the NTPs by a linker arm.
 10. The method ofclaim 1, wherein the multisignal labeling reagent further comprises anon-inherent charged group that increases the aqueous solubility of thereagent.
 11. The method of claim 1, wherein the polymer comprises afirst partner of a first binding pair.
 12. The method of claim 11,wherein the first binding pair is a ligand/receptor, a hormone/receptor,biotin/avidin, biotin/streptavidin or an antigen/antibody.
 13. Themethod of claim 11, wherein the first partner of the first binding pairis biotin.
 14. The method of claim 12, wherein the polymer is apolynucleotide comprising more than one region that is complementary toa portion of the extended oligonucleotide.
 15. The method of claim 1,further comprising combining the multisignal labeling reagent with atarget molecule such that the multisignal labeling reagent is bound tothe target by the first reactive group or the first partner of the firstbinding pair.